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1 =head1 LICENSE
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2
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3 Copyright (c) 1999-2012 The European Bioinformatics Institute and
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4 Genome Research Limited. All rights reserved.
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5
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6 This software is distributed under a modified Apache license.
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7 For license details, please see
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8
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9 http://www.ensembl.org/info/about/code_licence.html
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10
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11 =head1 CONTACT
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12
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13 Please email comments or questions to the public Ensembl
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14 developers list at <dev@ensembl.org>.
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15
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16 Questions may also be sent to the Ensembl help desk at
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17 <helpdesk@ensembl.org>.
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18
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19 =cut
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20
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21 # Ensembl module for Bio::EnsEMBL::Variation::ReadCoverage
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22 #
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23 # Copyright (c) 2005 Ensembl
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24 #
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25
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26
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27 =head1 NAME
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28
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29 Bio::EnsEMBL::Variation::ReadCoverage - A coverage reagion for a read.
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30
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31 =head1 SYNOPSIS
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32
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33 # Read coverage feature representing a genomic region covered by 1 read
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34
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35 $rc = Bio::EnsEMBL::Variation::ReadCoverage->new
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36 (-start => 100,
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37 -end => 200,
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38 -slice => $slice,
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39 -level => 1.
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40 -sample => $individual);
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41
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42 $rc = $rc->transform('supercontig');
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43
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44 print $rc->start(), "-", $rc->end(), "\n";
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45
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46
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47 =head1 DESCRIPTION
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48
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49 This is a class representing the read coverage information
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50 from the ensembl-variation database. A ReadCoverage behaves as any other Ensembl feature.
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51
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52 See B<Bio::EnsEMBL::Feature>.
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53
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54 =head1 METHODS
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55
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56 =cut
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57
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58 use strict;
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59 use warnings;
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60
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61 package Bio::EnsEMBL::Variation::ReadCoverage;
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62
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63 use Bio::EnsEMBL::Feature;
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64 use Bio::EnsEMBL::Utils::Exception qw(throw warning);
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65 use Bio::EnsEMBL::Utils::Argument qw(rearrange);
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66
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67 our @ISA = ('Bio::EnsEMBL::Feature');
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68
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69
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70 =head2 new
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71
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72 Arg [-ADAPTOR] :
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73 see superclass constructor
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74
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75 Arg [-START] :
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76 see superclass constructor
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77 Arg [-END] :
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78 see superclass constructor
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79 Arg [-SLICE] :
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80 see superclass constructor
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81
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82 Arg [-LEVEL] :
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83 int - the number of times the region represented by start and end has been seen
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84
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85 Arg [-SAMPLE] :
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86 Bio::EnsEMBL::Variation::Individual - the individual
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87 in which the allele was recorded
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88
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89 Example :
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90 $rc = Bio::EnsEMBL::Variation::ReadCoverage->new
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91 (-start => 100,
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92 -end => 100,
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93 -slice => $slice,
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94 -level => 1,
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95 -sample => $individual);
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96
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97 Description: Constructor. Instantiates a new ReadCoverage object.
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98 Returntype : Bio::EnsEMBL::Variation::ReadCoverage
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99 Exceptions : none
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100 Caller : general
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101 Status : At Risk
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102
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103 =cut
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104
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105 sub new {
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106 my $caller = shift;
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107 my $class = ref($caller) || $caller;
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108
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109 my $self = $class->SUPER::new(@_);
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110 my ($level, $individual) =
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111 rearrange([qw(LEVEL SAMPLE)], @_);
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112
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113 $self->{'level'} = $level;
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114 $self->{'sample'} = $individual;
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115
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116 return $self;
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117 }
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118
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119
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120 =head2 level
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121
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122 Arg[1] : int $newval (optional)
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123 The new value to set the level attribute to
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124 Example : $depth = $obj->level();
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125 Description : Getter/Setter for the level attribute. The level is
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126 the number of times this feature has been seen in the genome
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127 ReturnType : int
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128 Exceptions : none
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129 Caller : general
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130 Status : At Risk
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131
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132 =cut
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133
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134 sub level{
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135 my $self = shift;
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136 return $self->{'level'} = shift if (@_);
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137 return $self->{'level'};
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138 }
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139
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140
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141 =head2 sample
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142
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143 Arg [1] : Bio::EnsEMBL::Variation::Individual $newval (optional)
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144 The new value to set the sample attribute to
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145 Example : $individual = $rc->sample();
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146 Description: Getter/Setter for the individual attribute
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147 Returntype : Bio::EnsEMBL::Variation::Individual
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148 Exceptions : throw on incorrect argument
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149 Caller : general
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150 Status : At Risk
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151
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152 =cut
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153
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154 sub sample{
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155 my $self = shift;
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156
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157 if(@_) {
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158 if(!ref($_[0]) || !$_[0]->isa('Bio::EnsEMBL::Variation::Individual')) {
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159 throw('Bio::EnsEMBL::Variation::Individual argument expected.');
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160 }
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161 $self->{'sample'} = shift;
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162 }
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163
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164 return $self->{'sample'};
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165 }
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166
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167 1;
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